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Whitehead Group Contributes SNP--Discovery Technology To Consortium


CAMBRIDGE, Mass.--The Whitehead Functional Genomics Consortium, made up of Millennium Pharmaceuticals, Bristol-Myers Squibb, Affymetrix, and the Whitehead Institute for Biomedical Research, announced that it has allowed the SNP Consortium to use its technology for identifying single-nucleotide polymorphisms (SNPs) at no cost. The SNP Consortium, established earlier this year by 10 major pharmaceutical companies and the Wellcome Trust, is funding an effort to create a map of SNPs in the human genome.

The Whitehead consortium has applied for a patent on what it calls reduced representation technology, which it expects to speed the discovery process used by the SNP Consortium. Reduced representation, developed at Whitehead last year, fragments DNA from multiple sources into subsets by size, reducing complexities associated with screening each set for the presence of SNPs.

Millennium, Bristol-Myers Squibb, and Affymetrix formed the consortium in 1997 to fund a five-year research program in functional genomics at Whitehead under the leadership of Eric Lander, director of the institute's genome center.

The companies have committed a total of approximately $8 million a year for five-years. The arrangement also gives the institute access to Affymetrix and Millennium technologies. The three enterprises will apply Whitehead's developments to their businesses and to basic biomedical research.

Already, the companies are looking forward to the completion of the SNP Consortium's map. "A publicly available, high-quality SNP map will enhance Millennium's effort to create diagnostic and pharmaceutical products that address the cause, not merely the symptoms, of major diseases," commented Frank Lee, Millennium's chief technology officer. However, said Lee, it's important to remember the SNPs themselves are "just one component of the process. Having a large set of random SNPs mapped onto the genome is necessary, but by no means the most important piece of the process."

Members of the Whitehead consortium decided that its reduced representation technology could be given royalty-free to the SNP Consortium because it is largely an enabling technology rather than one that would lead directly to products and product sales, maintained Lee. "It allows you to get a representation of the entire genome without having to work with the complexity of the entire genome," he explained.

David Wang, senior research investigator in Bristol-Myers Squibb's department of applied genomics, said the technology being contributed to the SNP project uses reduced genomic libraries where the libraries represent about 20-30 percent of the human genome. "If you can make such libraries from multiple individuals and you can randomly sequence the reduced genomic libraries up to a certain coverage, the SNPs can be identified by comparing overlapping sequences from different chromosomes, which, because we have a library, will be made from multiple individuals," he explained. Wang is also chairman of the scientific advisory committee for the SNP Consortium.

--Matthew Dougherty

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